They are "based" on that chipset because it "HAS" it. But a motherboard is comprised of much more then just the chipset. This is why one motherboard is different from another, but both are "based" on the same chipset. But all the rest is different.
Here is how to go about building your system:
Step 1) What will you do with it? What is the MOST intense thing? This would be like gaming (half life 2, Battlefield2 etc...). CAD design? Movie production? Audio encoding?
Step 2) Pick a processor. A very and debatable suggestion is: if you are gaming, go AMD, if you are processing (CAD, audio, encoding etc) go Intel.
Step 3) Pick a motherboard to support the processor you want. If you go with the AMD, perhaps get a motherboard with the NForce3 Ultra chipset. This is for Socket 939 Athlon 64-bit CPU.
Step 4) Once you deside what CPU to go with, browse a shopping site like all our favorite,
www.newegg.com or
www.zipzoomfly.com, and search by that CPU socket.
Step 5) Once you choose a motherboard that has the features you want, read the reviews!
Basically you need to pick out these parts, usually in this order:
1) CPU
2) Motherboard
3) RAM
4) Video
5) Hard Drives
6) Optical Drives
7) Throw in a floppy!
8) Find a case you like that has a good power supply (at least 350watts)
When deciding what parts to buy, it all depends on the motherboard! For example: If the motherboard has PCI-X and NOT AGP, you will have to buy a PCI-X video card. So choose your video card after you know what motherboard you get.
Or maybe choose a hard drive based on what the motherboard gives you, IDE or S-ATA? Go RAID?
And for a couple links, perhaps check out this motherboard:
http://www.zipzoomfly.com/jsp/ProductDetail.jsp?ProductCode=241143
And this CPU:
http://www.zipzoomfly.com/jsp/ProductDetail.jsp?ProductCode=80701-5
Notice how the Motherboard and CPU match the socket (939). Also notice the chipset (nForce3 Ultra). Of course, you will find this chipset on many other boards from many other manufacturers. Also notice that the nForce3 has an AGP 8x/4x slot, but similar boards with nForce4 has PCI-X and NOT AGP. This determines your video card requirements.
Anyways, that is my take on it. Hope you got a pinch of knowledge out of this thread!